Linux is struggling on the desktop because it only has a small number of "great" apps, according to the Gnome co-creator. Miguel de Icaza, co-creator of the Gnome desktop, told tech journalist Tim Anderson at the recent Windows 8 Build conference "When you count how many great desktop apps there are on Linux, you can probably name 10," de Icaza said, according to a post on Anderson's IT Writing blog. "You work really hard, you can probably name 20. We've managed to p*** off developers every step of the way, breaking APIs all the time."

Linux desktop doesn't need any of the prorietary MS apis to sort out its developer story.
What is needs is stable, modern, systemwide OO api (best if managed). All that could be build on top of CLR without even touching any of MS IP tainted parts.
Best would be if somebody managed to seamlessly integrate QT and CLR (add something like pInvoke for QT objects), to get native support sorted out.

The answers so far for system level integration was: use C abi or sockets, technologies outdated for app integration 2 decades ago.